Copitarsia decolora (Guenée) is a widely distributed, highly polyphagous pest found throughout Central and South America. We examined multiple populations of C. decolora with the mitochondrial gene cytochrome oxidase I (COI). We also investigated morphological variation in adult males sampled from these populations. COI evidence suggests that C. decolora is comprised of two cryptic lineages and is paraphyletic with respect to the Chilean C. naenoides (Butler). These two lineages, which are not completely geographically isolated, display high divergence in COI sequences compared with other members of Copitarsia and other insect pest species in general. Furthermore, these lineages also possess slight morphological differences in male genitalia; however, supporting information is necessary before the taxonomy of this species is revised.